There is no absolute etiquette on this and unless there is a note on the invitation, then my inclination would be to give a present and a card to the child who invited me only. I might give a card to the other child though, or even a small gift like a ladybird book or some bubbles or something.
Sorry that's not much help is it?!
DD had a joint party at nursery with a boy i the same nursery class, a lot of the children were joint friends but some were only invited by either DD or this boy, although both names were on the invitation. In my experience, the mums of girls bought presents for both the children while the mothers of the boys only tended to buy for the boy, assuming they were invited by him, not by both of them. At 4 though they really didn't notice though, they were too busy having fun!
We tend to operate on a basis of buying for the child(ren) you know -- so if you know both children give two gifts but if you only know one child (and I'd include having met the other once at a party as only knowing one child) then only give one gift. DS had a joint party with a friend of his and that seemed to be what other parents were doing too.